The cost of efficiency in energy metabolism.

In a universe being dragged into disorder by the second law of thermodynamics, living cells must expend energy to maintain their complex organization. In addition to providing a carbon source for biosynthesis, the classical Embden–Meyerhof–Parnas (EMP) and Entner-Doudoroff (ED) pathways help to satisfy this energetic demand by generating ATP during glucose metabolism (1). Based on simple stoichiometry of reactants and products, the EMP pathway appears, at first blush, greatly preferable to the ED pathway, yielding twice as much ATP per glucose. If glucose breakdown and energy conservation are tightly coupled, why is the less-efficient ED pathway so prevalent? What has kept prokaryotic life in its entirety from casting off the ED pathway in favor of the more profitable EMP pathway? In PNAS, Flamholz et al. (2) address these questions by drawing on thermodynamics, enzyme kinetics, mathematical optimization, and genomics. The first stage of glycolysis is characterized by an investment of ATP to phosphorylate glucose, which, so primed, is cleaved into two three-carbon intermediates (Fig. 1). The cell recoups its investment in the second phase of glycolysis (known as “lower glycolysis”), where oxidation of three-carbon intermediates directly generates ATP. Although the ED and EMP pathways overlap in part, they conspicuously differ in the number of threecarbon intermediates shunted down lower glycolysis. In the EMP pathway, glucose is phosphorylated twice, consuming two ATP, and both three-carbon intermediates (glyceraldehyde 3-phosphate, or G3P) enter lower glycolysis to produce two ATP each. In the ED pathway, glucose is only phosphorylated once, consuming one ATP, before being cleaved into one G3P and one pyruvate. The single G3P yields two ATP as in the EMP pathway, but pyruvate bypasses the bulk of lower glycolysis, foregoing ATP production. Thus, despite both pathways starting and ending with the same amount of glucose and lactate, the EMP pathway manages to extract two ATP per glucose, the ED pathway only one. The ED pathway is thought to predate the EMP pathway (dominant among eukaryotes) in the evolutionary timeline (3). Is the EMP pathway simply a fine-tuned adaptation of the ED pathway optimized for energy conservation, or does high ATP yield come at a cost? Flamholz et al. (2) highlight a tradeoff that logically arises between a glycolytic pathway’s ATP yield and thermodynamic driving force. Free energy released during glucose breakdown can drive ATP synthesis, providing energy currency to the cell, or dissipate as heat, making the overall pathway more thermodynamically favorable (albeit less efficient) (4). By harvesting more free energy as ATP than the ED pathway, the EMP pathway operates closer to equilibrium (5). Conversely, production of pyruvate so early in the ED pathway–a highly exergonic reaction–dissipates ample free energy, leaving little for ATP generation. Flamholz et al. (2) show that, even if metabolites assume concentrations that make the least favorable reactions in each pathway as exergonic as possible, the EMP pathway faces much tighter thermodynamic bottlenecks than the ED pathway. Although a simplified representation of linear metabolic pathways (as in Fig. 1) conveys their tendency to proceed in the forward direction, it glosses over bottleneck reactions that are only weakly favorable, with a negative free-energy difference close to zero. Such highly reversible reactions can easily clog a pathway, limiting if not preventing forward flux. Despite its thermodynamic obstacles, the EMP pathway is known to function effectively in living cells. How to reconcile these two contrasting observations? And how would we expect a microorganism to cope physiologically with a thermodynamic bottleneck? Flamholz et al. (2) address these questions by considering the enzyme production costs associated with each pathway.